FitViewer for context based zoning and cropping of cryo-EM maps using pseudo-atomic models fitting into cryo-EM electron density maps of lattice based DNA origami structures
start the interactive Jupyter-Notebook by executing the following command from the repository directory:
jupyter notebook viewertool.ipynb
Step by step instructions are provided in the Jupyter notebook
FitViewer is currently distributed as a Jupyter Notebook. It requires an ipytohn kernel with the following dependencies:
python >= 3.8.0
dnaFit DNA Origami atomic model package
required PyPI packages:
ipywidget
ipython
jupyter
FitViewer relies on the MDAnalysis package for reading trajectories or coordinate files, mrcfile for handling cryo-EM data, and DNA Origami design files generated using cadnano
When using FitViewer in published work, please cite the following paper:
Kube, M., Kohler, F., Feigl, E. et al. Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Nat Commun 11, 6229 (2020). https://doi.org/10.1038/s41467-020-20020-7